Mosquitoes Culex pipiens is a major vector species for Japanese encephalitis and filariasis in China, and it is an important vector of West Nile Virus in the USA. Vector control is an important means of mosquito-borne disease prevention and management. Pyrethroid insecticide is currently being promoted worldwide for disease vector control because of their high efficacy, rapid rate of knockdown, and low mammalian toxicity. Due to wide- spread and improper use of insecticides, resistance to pyrethroids is very prevalent in Cx. pipiens mosquito species in China. The long-term goal of this research is to elucidate the genetic and molecular mechanisms of pyrethroid resistance in Cx. pipiens mosquitoes, and to develop more accurate and cost-effective resistance detection methods that are applicable to field samples. During the past three-year granting period, we have established deltamethrin resistant strains of Cx. pipiens, characterized novel genes associated with deltamethrin resistance in Cx. pipiens, developed PCR-based knockdown resistance (kdr) mutation detection methods and conducted quantitative trait loci mapping for pyrethroid resistance. Because the classic genetic mapping study in our previous studies cannot identify genetic transcripts differentially regulated between susceptible and resistant individuals, this renewal application will use high-throughput transcriptome analysis and population genetic approaches to determine the relationship between pyrethroid resistance at organismal level and transcription activity and gene nucleotide polymorphisms at molecular level. Here we focus on insecticide resistance at the organism level because mosquitoes may possess compensatory mechanisms under the selection by insecticides. Studying individual genes in cell lines will not reveal resistance at the organismal level because it ignores gene-gene and gene-environment interactions. The specific aims are: 1) to identify the major candidate genes for resistance to deltamethrin in Cx. pipiens using transcriptome analysis, 2) to determine the function of the candidate genes in pyrethroid resistance; and 3) to establish association between pyrethroid resistance at organismal level and gene polymorphisms and transcription activity at molecular level. We anticipate that this research will significantly enhance our understanding of resistance to pyrethroid insecticides in Cx. pipiens mosquitoes. The knowledge from this application will greatly facilitate the development of new resistance diagnostic methods for this important disease vector in China and the world.